0.9.0-SNAPSHOT-1

Basic field dependence on rate equations has been implemented.

0.8.0

Ported the build system to Maven.

Package refactoring and a new RPC server

Contains ALICA v0.2.5

Added

• An RPC server was created that allows for remote control of the simulation over the network.
• A new image abstraction layer called ImageS that separates image data logic and display from the SASS core code.

Changed

• The package layout was restructured and simplified to make it easier for newcomers to understand and to better consolidate components that were added after the original layout was devised.
• The ImageGenerator interface was renamed to Simulator, while the original Simulator class was renamed to ImageJSimulator and moved down one directory to the internal package.
• The SimEngine class was renamed to DefaultSimulator and moved to ch.epfl.leb.sass.simulator.internal.

Bug fix for missing ALICA class

Contains ALICA v0.2.5

Added

• A convenience method named getFrameInfo() was added to FrameLogger (called FrameInfo) that returns a single data structure containing the per-frame-information about each emitter.

Changed

• Bulky ALICA_dev.jar was replaced by ALICA_for_SASS_v0_2_5.jar which reduced SASS jar size to 8MB.

Usability improvements

Contains ALICA v0.2.5

Added

• You can now save and load simulation settings from the GUI.
• There is now a FrameLogger for recording the frames that a fluorophore is on. This produces larger log files than the StateLogger, but does not require post-processing to extract the frame numbers.
• It is now possible to generate random background patterns using GenerateRandomBackground.
• Emitter positions and state transitions may now be saved from the GUI.

Changed

• A status report on PSF calculation is now output to the console for every 5000 calculations.
• Each simulation output is now displayed in its own plot for easier tracking of the simulation parameters over time.

Fixed

• Fixed a cropping issue with the self-tuning PI controller dialog on Linux.
• The GibsonLanniPSF cache is now erased everytime a new builder is created for this PSF type. This prevents caching calculations done for previous simulations.
• The Save... button in the Initialize Simulation window is now properly displayed as a Save dialog.
• The latency bug that caused a pause during every tenth simulation frame in GUI mode has been fixed. The latency came from updating the original status plots, which have been changed in this version.
• Loggers now properly check for filename collisions to prevent overwriting previously saved data.

Removed

• The button that allowed saving the simulation outputs in the GUI has been removed because it didn't work. This functionality may be reimplemented in the future if there is interest.

Improvements to the Gibson-Lanni PSF

v0.5.1

Contains ALICA v0.2.1

Changed

• The GibsonLanniPSF now caches computation results to avoid repetitive calculations.
• The GibsonLanniPSF.Builder now has a solver() method for setting the solver for the Bessel function coefficients. It accepts either "svd" or "qrd" as arguments. (SVD stands for singular value
  decomposition and QRD stands for QR decomposition.)
• The GibsonLanniPSF.Builder also now has a resPSFAxial() method for determining the spacing between axial planes of the computational grid.
• The GibsonLanniPSF.Builder also now has a maxRadius() method for setting an upper limit on the size of the area that the PSF is drawn onto. Reducing it can significantly speed up simulation times.

Fixed

• PSF instances are not, in fact, immutable because their fields are not final.

API Overhaul

v0.5.0

Contains ALICA v0.2.1

Added

• There is now a GibsonLanniPSF for modeling realistic 3D PSF's and that can account for details such as sample, coverslip, and immersion media refractive indexes and thicknesses.
• A PSFBuilder interface was added to allow for a PSF to be built at various times during the simulation, rather than all at once. This addition is necessary to account for axial stage positions that might change during the simulation.
• Added a Stage component to represent the state of the microscope stage.
• Added functionality through the BackgroundCommand to build custom backgrounds for the simulations.
• Added a Microscopeclass to replace Device. This class integrates the various new and refactored components.
• Added a set of Dynamics classes to separate fluorophore dynamical systems from their creation logic.

Changed

• Major API changes were made in this version. The purpose was to assign properties to components in a way that better matched a real microscope (e.g. a camera should not have a wavelength). The change to a builder based API is intended to to decouple all the components and make the scripting easier.
• PSF instances are now immutable.
• Optics-based logic was moved from the camera to a new Objective class, whereas the original camera logic was moved to a new Camera class in the components package.
• The Laser has been moved to the components package.
• Fluorophore generation is no longer setup by the user but executed by the microscope.
• Obstructors are now setup by the microscope as well. GoldBeads are now created by a ObstructorCommand object.
• FluorophoreProperties now has a wavelength property. The wavelength property was removed from the camera.

Refactor PSF generation

v0.4.0

Contains ALICA v0.2.1

Added

• STORMsim now has a method wrapper called incrementTimeStep() which advances the simulation by one frame without recording an image to the stack.
• PositionLogger object for recording the fluorophores' initial positions in x, y, z to a file.
• A PSF interface has been created to more easily extend the number of PSF models used by SASS.
• A Gaussian3D PSF class was added for modeling PSF's as a through-focus Gaussian beam.
• Added new methods to FluorophoreGenerator and scripts for creating 3D fluorophore distributions.

Changed

• The Emitter, Fluorophore, and Camera API's have been changed to decouple the camera logic from light sources.
• The PSF creation routines originally found in the Emitter class are now located in a Gaussian2D class that implements the PSF interface.
• PositionLogger and StateLogger now extend an AbstractLogger base class.
• PositionLogger and StateLogger now reside in the package ch.epfl.leb.sass.simulator.loggers.

Implemented state transition logging

v0.3.0

Contains ALICA v0.2.1

Added

• StateLogger object for recording each fluorophore state transition
  and the time at which it occurs.
• Example script example_run_generator_logging.bsh which
  demonstrates how to log the groundtruth output from a simulation and
  save the results to a .csv file.

Fixed

• Fixed a bug preventing the opening of a background file on Linux/Mac
  OS that was caused by a hard-coded backslash file separator
  character.

Removed

• Removed the script example_run_generator_moving_from_csv.bsh and
  made a comment about how to implement trajectory loading from an
  external file in example_run_generator_moving.bsh.

Bug fixes for the camera noise model and fluorophores

Contains ALICA v0.2.1

Added

• Electron multiplication (EM) gain and camera baseline parameters.

Fixed

• The camera noise model was improperly accounting for electron
  multiplication noise. This is now fixed and encompasses both EMCCD's
  (by setting the EM gain to a non-zero value) and sCMOS (by setting
  the EM gain to zero.)
• A problem preventing the creation of new dStormProperties
  fluorophore models.